rs4900229

Variant names:

• chr14-94370192-C-T
• rs4900229

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.182 in 150,602 control chromosomes in the GnomAD database, including 1,144 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (1144 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.98
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27411 AN: 150486 Hom.: 1138 Cov.: 34

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.202

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.182 AC: 27431 AN: 150602 Hom.: 1144 Cov.: 34 AF XY: 0.183 AC XY: 13471 AN XY: 73602

African (AFR) AF: 0.129 AC: 5347 AN: 41298

American (AMR) AF: 0.153 AC: 2328 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 775 AN: 3422

East Asian (EAS) AF: 0.291 AC: 1466 AN: 5034

South Asian (SAS) AF: 0.367 AC: 1687 AN: 4598

European-Finnish (FIN) AF: 0.158 AC: 1660 AN: 10536

Middle Eastern (MID) AF: 0.254 AC: 72 AN: 284

European-Non Finnish (NFE) AF: 0.200 AC: 13429 AN: 67248

Other (OTH) AF: 0.208 AC: 436 AN: 2092

Alfa AF: 0.194 Hom.: 201

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.046
DANN	Benign	0.82
PhyloP100		-4.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4900229; hg19: chr14-94836529; COSMIC: COSV73618979;